chr20-55790646-G-A

Variant names:

• chr20-55790646-G-A
• rs6092176

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.409 in 152,052 control chromosomes in the GnomAD database, including 16,289 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (16289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62151 AN: 151934 Hom.: 16257 Cov.: 33

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0442

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.373

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.409 AC: 62226 AN: 152052 Hom.: 16289 Cov.: 33 AF XY: 0.400 AC XY: 29733 AN XY: 74316

African (AFR) AF: 0.744 AC: 30877 AN: 41478

American (AMR) AF: 0.277 AC: 4233 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3468

East Asian (EAS) AF: 0.0441 AC: 228 AN: 5168

South Asian (SAS) AF: 0.231 AC: 1115 AN: 4826

European-Finnish (FIN) AF: 0.290 AC: 3057 AN: 10542

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20367 AN: 67974

Other (OTH) AF: 0.369 AC: 780 AN: 2112

Alfa AF: 0.329 Hom.: 17232

Bravo AF: 0.421

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6092176; hg19: chr20-54365702;